3VQV | pdb_00003vqv

Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in complex with AMPPNP (re-refined)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3VQW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.8	293	Na/Cacodylate, MgCl2, PEG4000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.35	63.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.876	α = 90
b = 104.876	β = 90
c = 70.433	γ = 120

Symmetry
Space Group	P 64

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 210		2005-02-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.0000	Photon Factory	AR-NW12A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.9	50	99.8	0.089		8		34806

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.93	99.5		0.45		4.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3VQW	1.9	42.07	33041	1750	100	0.1882	0.18657	0.19	0.2191	0.22	RANDOM	38.945

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-0.7	-0.35		-0.7		1.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.637
r_dihedral_angle_4_deg	20.486
r_dihedral_angle_3_deg	17.916
r_dihedral_angle_1_deg	6.095
r_scangle_it	4.783
r_scbond_it	2.925
r_mcangle_it	2.08
r_angle_refined_deg	1.706
r_mcbond_it	1.186
r_nbtor_refined	0.315

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.637
r_dihedral_angle_4_deg	20.486
r_dihedral_angle_3_deg	17.916
r_dihedral_angle_1_deg	6.095
r_scangle_it	4.783
r_scbond_it	2.925
r_mcangle_it	2.08
r_angle_refined_deg	1.706
r_mcbond_it	1.186
r_nbtor_refined	0.315
r_symmetry_hbond_refined	0.256
r_symmetry_vdw_refined	0.228
r_nbd_refined	0.225
r_xyhbond_nbd_refined	0.225
r_chiral_restr	0.12
r_bond_refined_d	0.017
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2095
Nucleic Acid Atoms
Solvent Atoms	246
Heterogen Atoms	33

Software

Software
Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.